Marine stadium is great especially overnight as the view is amazing.
Boca Chita on week days is great, not in summer due to mosquitoes. Eliot is one of our favorite as the water is nice and clear and if you stay 1/4 mile off shore bugs aren't bad in summer.
No name Harbor, at the top of key biscayne is nice as you have access to many trails and Crandon beaches. Again, busy on week end. No bigs in summer as they spray on KB unlike biscayne national park
The KB sand bar, aka nixons, next to KBYC is always a good spot too, again busy on week end.
I ve been living, playing and working on biscayne bay for 25 years now and still haven't found anything like anywhere else...