I would choose the GameBoy due to the fact that, even if Nintendo releases an N64 Mini, they will never be able to get the licenses to include most of those that are, for me, the best games of that console, namely GoldenEye 007, Conquer's Bad Fur Day, Banjo-Kazooie, Turok, Sin & Punishment, Star Wars Episode I: Racer, Star Wars: Rogue Squadron and Mischief Makers.
Apart from that, I am not sure about the prices of N64 stuff in the West, but at least in Japan, it is cheaper to buy an N64 bundled with a dozen good games than getting any console of the Classic Mini series, whereas the best games for the GB/GBC are starting to get pretty expensive around here...