It's sort of a crapshoot between those two places.
While Chinatown will probably be better priced as far as collectible goes, many of them are basically marred with lots of questionable quality things. Japantown is going to have much more of the authentic stuff, but pricing wise, it's hit or miss for the most part. Not saying you can't find anything authentic collectible wise in Chinatown, but depending on the store, the quality might not always be the same. I think it really all comes down to exactly what you mean by collectibles. Touristy collectibles about SF, or collectibles as in gaming stuff, anime stuff, etc.?
If you just need a simple plan, just go to Marufuku Ramen in the Japan Center in Japantown. This will basically get you to the heart of Japantown, and then you can wander around from there. However, if you like other options, depending on your accessibility to BART, there's some other authentic places you can go to.
Any chance you could maybe provide some more details on your specifics of location, transportation, and also other things that might help narrow down the specifics to get you some better recommendations for your needs?
Also, is this for today, tomorrow, Monday, etc.