In my experience of experimenting with 2.4ghz systems over water for our type of usage, I would say that it does not matter - to quite some range - if the antenna on the boat is below the waterline.
How so? The boat is at water level, but on a typical pond, even if seated, you will be transmitting from at least two feet above water level, so the TX antenna will be 'looking' into the boat, below it's waterline, for quite some distance (150yds+ is not unusual in my experiments).
How can you prove the effect? Take the boat out a fair distance with the RX antenna below the waterline whilst TXing from a standing position. Lower the TX until the boat's control is lost (you DID set the failsafe didn't you?).
Stepping aside from that momentarily, I find that the best orientation for Spektrum antennas is a 45 degree angle upwards/downwards and northwest/southeast or northeast/southwest across the boat - It gives the best balance of reception when travelling abeam and fore/aft.
Answering the OP somewhat, as long as some part of the antenna is above the waterline of the boat, and you are not operating from the prone position, you'll be fine to around 100yds and probably more, in my experience.
-Rob