There are Peanuts strips - not all of them, but more than a couple - which I'd pit against Calvin and Hobbes in terms of depth. F'rinstance, Charlie Brown, when attempting to kick the football, was quite aware that he would fail and often dealt with why he was trying anyway. Were I arguing for the superiority of Peanuts I'd've probably worked an angle that anything Calvin and Hobbes did well, Charlie Brown did first.
The only exception to this that I can come up with is Waterson's expansive Sunday format. I'll always love the guy for fighting the shrinking size of funnies.
My go-to wouldn't've been either comic, though. For me the connundrum will always be between Far Side and Bloom County. The former mastered the one-panel strip, arguably introduced the world to geek humor, paving the way for Dilbert and subsequent web-comicry; the latter, IMHO, predated C&H's hallmark large-scale Sunday strip, replete with dream-like surrealism.