You comment about smaller islands brings to mind both Woman and Man keys. Man Key is better since it is really a bunch of small keys with passages both in and around them, but both have small beaches. Saying that, look at the Javacat
Or the Echo II...
(Make sure you specify at least 4, but better, a 6 hour Charter)
Both of these can get into the Sanctuary where these small islands are located, and you should indicate your interest if you book either.
But also look at Breezin' Charters...
Breezin's draft is too much to get into the Sanctuary but captain Dees will take you out to the reef to snorkel and just hang out, and will stretch a four hour charter into an afternoon with a sunset on the way in.
Any of these three, as well as Take MeThere, will give you all a great day out of Key West. But this can be all confusing so I can post a few photos of what one of these trips is like if you want.
Edited: 9:26 pm, March 04, 2013