The best I can tell you on this is if you are trying for more HP, the 350 has it hands down. FYI, the 88 350 very possibly has a factory roller cam which is a major plus. You can pick up an LT1 high performance cam that will fit in the engine, even better, the high performance LT1 Hotcam. That, coupled with a good set of roller rockers and a decent intake and carb set-up will plant a smile on your face. Of course, the hotcam will require heavier valve springs.
As far as being better, it would be a toss-up, but I definitely would choose the one with roller cam if it had it. Some of the Chevrolet engines came from the factory with a stock roller cam in 87.