I've used clear silicone caulk (like the kind used for bathrooms and windows) before and had no issues and it turned out looking pretty good. A couple things to take note of though:
-Paint the base your sea color before applying the caulk, then attach your ship. This will actually give the water some depth.
-Keep the caulk thin, if it gets really thick then you'll have some cloudiness.
-If you do end up with cloudiness, and where you want to paint wake, use white enamel paint. It will bead up a little which actually makes it look like real sea foam. Be ready to do multiple coats of white.
I would recommend playing with it a bit on some scrap material (cardboard, wood, styrene, etc.) and see if you like it before you dismiss it, caulk is pretty inexpensive.
Groot