Please keep in mind my list will only consist of series that I have read, so your favorite may not be on this list.
I remember picking up the first volume and rolling my eyes at all the nonsense going on, but as I went deeper into the manga I really got into the story and was invested into the characters' struggles. Rosario Vampire is a supernatural series with a school life atmosphere as the setting is an academy for monsters. The series has a double plot line, both being well fleshed out and keeps the story exciting. Yes, it was silly at times but I got used to it after reading it for a while. My husband doesn't read manga so I told him about this series and we found the anime. I was not a fan of the anime at all! Too much fan-service, almost to the point where that was the main focus. Read the manga to get the full experience of the story, it's well worth reading. Great character designs for cosplay may I add.
The Sacred Blacksmith
This isn't consider too shounen, but I can surely tell you it's not shojo material. So I'm putting this series in shounen as there are a lot of action/adventure elements in the series. I would have never even picked up this manga if it wasn't for one of my guy friends suggesting it to me (the same friend also recommended Rosario Vampire). My friend knows I hate fan-service in anime and manga but when he tells me I'll like a manga series I'll usually try it out because he knows I'm a sucker for a good story. That's exactly what you get in The Sacred Blacksmith. It's about this girl, Cecily Campbell, who is part of the knights. She's trying to prove herself to everyone and just trying to protect her town from evil people and demons that threaten their way of life. She's obsessed with swords even though she doesn't know how to properly use one, but befriends a demon sword that helps her through her fights. The story gets way more involved as this is also part of the fantasy genre, but if I tell you more I feel like the excitement of the story would be lost. Go into the series knowing you're going to have a good time. Keep in mind that this series is still ongoing with a completed anime that stops short.
Cage of Eden
I feel like this is an underappreciated manga series because I don't hear many people talking about it. I picked up this manga on accident, thinking it was another series that another friend told me about and got the title names confused. I'm so happy for my mistake. The story is amazing! If you like detective/mystery series with a survival theme, then this is the manga series for you. This series doesn't have an anime which I wouldn't mind seeing one made but the manga is great. It's about this class coming back from a school trip with a bunch of other people but their plane crashes on a deserted island that is not marked on any map. It's starts out sounding like the TV show Lost, but then you discover the island actually has wildlife on it that is from millions of years ago. It's a very dangerous island. The students and random people from the plane have to fight to survive while trying to figure out who would make an island for dangerous, extinct animals (and I'm talking pre-historic). I love the mystery and survival aspect of the series. Give it a try if you think it's something you'll like. This is a 21 volume series that has ended.
Yep, Pokemon! If you've only played the games or watched the anime you are missing out. The manga is very different from both. Viz has labeled it as a children's manga series but I think it shouldn't be. The manga has a dark tone, way different from the anime and partly different from the video games (fan theories make the game terrifying at times). The manga hides nothing and just throws these dark themes into your face. (Sorry if I talk about the dark tone of the series a lot, I really appreciate darker stories). But not only that, but Red is a great character to follow around unlike the anime counterpart Ash Ketchem. I've only read the first set of the Pokemon manga series so I can't tell you how the whole series is but I can say that the first set that covers the Kanto storyline is a great read. You will be surprised at how different it is from the anime and video games.
Another underappreciated series is Bloody Cross. I first bought this series solely for the artwork (I've bought many bad manga just by looking at the art). I was glad to find out I picked up a really great series. This is another manga in the supernatural genre as the main characters are vampires and angels. I won't say much about the story because it'll give a lot away but the story is just a big war of these two groups fighting over powerful relics. It doesn't hurt that the series has a small love story in it. It's a relatively short series, at 12 volumes with no anime adaption. Probably won't get one as it is very unknown to the manga community.
Another ridiculous series when it comes to fan-service but is very intriguing. In every volume there is a recipe for a food they cook in the series. I find there focus on food very interesting since no other manga focuses in food in this way. If you love food and tournament series then this is the manga for you. The main character is in a competitive school for prodigy cooks. He is looked down upon for his family's local family restaurant as everyone else seems to be of a higher breed. The series just follows the main characters' "food wars," working his way up the ranks in his father's footsteps. This is a great series to watch in anime form too for those not a fan of manga.
Thank you for reading my shounen favorites! Like I said before, I don't read many shounen manga since it's just easier to watch the anime but these series I mentioned either did better than the anime versions or didn't even have an anime. I love a good story so you are in for a treat with these series I picked out. There are other great shounen manga out there that I either haven't read or I thought the anime did a great job adapting to the manga. If you have any recommendations for me you think I may like please leave the titles in the comments.