Here's a strat and counter.
If the Tom is exposing himself on a hill or open area, you can take it down with ELRMs, their range is 1500m. Raven, Owens, and Catapults have them. Especially if you're in a Cata, definitely use the jjs to your advantage. The Eoptics from the raven and owens is a really huge advantage here.
"But if i'm using an missile config with radar on, won't he just blow me to bits?"
Ah good question and thats the special strat, you need to be as close to the max range as possible. At lot of times Tom users don't pay any attention to targets that are on the max range of their radar since much of the time it's just targets fed to them via c3 that are "beyond" their range.
Launch then run while under passive to dodge the return fire if they got a bead on you.
For Tom users, they can only do this if you leave yourself exposed. Most of the time happens when Toms are used from the high ground.