Probably "choose tomatoes". When you talk about "picking" fruit, berries, etc, it typically implies the action of taking them off of the tree or bush. So, if someone told me they were "picking tomatoes", I would assume they are picking the tomatoes off of the tomato plant.
Here are some options you could use.
"I need to get some tomatoes."
"I need to buy some tomatoes."
"I need to pick up some tomatoes."
"I need to pick out some tomatoes." ("To pick out" something means "to make a selection from the options").