Thunderbolt. 90 BP and STAB, and being 100% accurate, should be enough to cover any Water or Flying types you meet. In-game, you pretty much want to brute force everything, so having your main attack constantly miss is pretty bad.
It really depends on your team. If your Pikachu is alone without any support, use Thunderbolt again. Unless you're using Raichu, Pikachu will probably be holding a Light Ball, which means you can't use any other items that might boost your accuracy or anything.
If you're using Pikachu as a Rain sweeper however, Thunder is definitely the way to go. It has 100% accuracy in rain.