Captain- Captain Kirk
Not only is he one of the best Captains in my opinion, but even without his weapons he's a brilliant strategist. A notable reference for this is the episode 'Arena', where he fights against a member of the Gorn.
1st pick- Donatello
I've always had a special spot for this particular hero in a half shell. Not only is he level headed, but he does machines (that's a fact jack!), and he's got a good understanding of biochemistry.
2nd pick- Kurt Wagner
The much needed comedian for the group! Nightcrawler offers a lot to a team. Not only can he effectively kick ass, but he can travel over great distances, and take his team along with him if the need arise.
3rd pick- Cassandra Cain
Not just the token girl on the team! She's trained alongside the best, and has demonstrated her abilities to work both off and on a team.
I picked this team mainly because I believe their personalities won't compromise their ability to work well together, and not to mention they're all badasses in their own right. I've noticed quite a lot of teams were made based on brute strength, and the creators often times didn't take into account how the team would react to each other, for example putting to leader types into a team can cause a lot of drama, and ultimately pull the team apart.