By stopping the waves at the source
These surface dwellers don't seem to know or care about this race. Of course, you can put up a shield, or breed sea monsters to deter approach, but that might actually make the land-folk more curious, and encourage them to come closer. When they find
Atlantis the thing being defended, all the while being encouraged by continued losses, the will find Aliens! a hostile, hidden force. I predict very fast escalation, if not straight-away nuclear strike. Not an optimal outcome. This is, of course a simplified timeline, but unless peace is reached very fast, a war of extinction is quite probable.
What would the average country with a sizable navy say, if they found that the Bermuda triangle is full of
dinosaurs things who have secretly developed genetic hacking to such an extent that they can breed dogs into guns? They would quite probably assume that targeted diseases, i.e. biological warfare, is only a short design process away, or even stockpiled. Some trigger-happy general or president might decide to keep this tech out of any potential terrorists or enemy countries, by destroying it.
I think that I've made it pretty clear that hiding is not a very viable option. Instead, I recommend one of two options:
The best defense is an indiscriminate offense
Since you can indeed breed things to such high usability, you could easily breed a perfect biological weapon (Just a few options). Or, you could go for a less overt option, and let them wipe themselves out. While hijacking a sub, and getting it to launch a nuclear missile would be quite difficult, there are other, similar options. If your ethics committee is OK with it, you could breed one of your own to be able to pass as human, and become a political leader who can start the war themselves.
If nuclear fallout is not a desired side affect, and neither is extinction, or even a race of slaves, you can always try
The best policy, honesty.
If it wasn't apparen't already, I'm assuming that the surface-dwellers have no idea you exist. If they do, then they have basically been dropping bombs on you. They asked for what's coming. However, you could try giving a few examples of why they don't want to do that. This might make you a few enemies, but if you make the demo impressive enough, they won't dare attack you. Or they might try their best to wipe you off the planet, but to be fair, they were already trying to do that anyway.
If they don't then the remedy is simple: Say hello. (This one has a more impressive "greeting" on the poster). How you go about doing this is up to you. You could breed a Kraken, and show up riding it into New York harbor. You could send Morse code through your specially bred whale orchestra. You could even go through Area 51. However you do it, eventually you will be able to go up to the UN, and demand that depth charges be banned.
For a more impressive, if more risky approach, secretly sponsor a splinter group to start along the violent route. Then urgently contact a group of politicians, warning them of the threat, gaining yourself some friends, but also sending the message that these things need to be stopped.
This also has the bonus of letting the community make space whales within the foreseeable future.