Hmmm, sounds a lot like my experience with skunks and tomatoes (imagine that, skunks like tomatoes!) But with your fence, maybe raccoons are the culprit, as they can climb.
One trick that has worked for me in the past is to sprinkle wood ashes on the tomato plants. And its good for the soil, too! Just don't overdo it and don't do it on a breezy day
Another suggestion could be live traps. I can rent them from my local hardware store, which is cheaper than buying them. Raccoons love canned dog food so use that for bait. Only quirk is that raccoons are nocturnal and so are skunks, which I imagine love dog food too.
DOOO check with your local DNR to make sure you can live trap and relocate critters.
Good luck and keep us posted
Thanks, Chris and Ernie!