Hello Sandy, Squirrels are digging holes because they think they buried seeds, acorns or the like in your yard last season. That should pass as soon there will be other things for them to eat.
I am not aware that squirrels eat tomatoes, you may have what is called a ground squirrel or 13 lined chipmonk feeding on your tomato fruits. If your tomato plants are being eaten it is not likely a squirrel. Rabbits, deer and groundhogs are a possibility. Rabbits will begin to graze on a lot of different plants as springs moves forward. There are some commercial deer and rabbit replellant products are pretty good.
Good Luck!
