I've read all of the PTerry's books and the entire Martin Song of Fire and Ice series.
They're completely different kinds of books. Martin is essentially writing in the traditional fantasy genre while shaking it up by turning a lot of its conventions on their heads. Pterry is essentially a satirist who uses the fantasy genre as a means of parodying
'roundworld' culture. (There's actually a lot more to him, but that's a simple summary).
If I had to choose between one, there'd be no contest. Pterry wins hands down. Martin's last two Fire and Ice books were exceedingly ponderous, unfocused, and, in many cases, just plain dull.
Pterry, on the other hand, has varied the themes and characters of his DW books over the years and, in many of them, has created incredibly intricate and profound examinations of religion, morality, power, belief systems, and history. There's not a single character Martin has created that comes even close to possessing the depth and complexity of Sam Vimes, and none of the hundreds of pages Martin has written about the religious beliefs of Westeros possesses any of the profound insights Pterry delivered in Small Gods.

