Which second move to my Shadow ball mewtwo

Like you had a choice there, haha. You may have to stick to whatever the game gives you when you run out of TMs. Just my experience at least, I burnt 17 TM going back and forth between moves I didn't want. Now I have 0 charge TM and raids don't drop them for me anymore.

Right, theoretically speaking ice beam and thunder bolt are the most useful.

For Raids, Ice Beam is the best choice. My Maxed 96% SB Mewtwo can be used now almost vs all Gen 4 Legendaries, except for Regigigas( it will be just boring Machamp Parties) and now for Heatran. Also when Groudon , Lati Twins, Rayquaza wil return, he will be useful :)

ShadowBall + Focus Blast if your gamestyle is attacking gyms, it's THE beast: anything Shadowball-resisting will be melted by Focus Blast.
Don't save your SB Mewtwo for Ultra, max it out, and then it can be used in Master too.
For Ultra, you have so many alternative

I wouldn't use M2 in Ultra, it's too glassy there.
For PvP either IB or TB are the most useful. They charge faster than SB so can win in a M2 battle and deplete the enemy shields more quickly. TB is also SE vs Kyogre and Gyarados while IB is SE vs Groudon and dragons, all regulars in Master league teams.

Don't use mewtwo in ultra League, he's much weaker than many other psychic alternatives at the same CP.

In master League, I'd recommend ice beam. Thunderbolt is also viable, but mostly just covers kyogre. Ice beam has a lot of coverage.