A nice way to say it is to use "thought" as a noun (as in, to have a thought) rather than the verb "thought" (past tense of "to think"):
Today I had as many thoughts of you as there are balloons on this shirt!
Otherwise, if you want to keep the verb, the correct way would be:
Today I thought of you as many times as there are balloons on my shirt.
But the second way sounds a bit awkward. Either way, it's a very nice thing to say to a friend! :)