i pick diego by a small margin.
if maradona gave sweet FA about his image, picking him would'nt cause to much controversy.
maradona played in a faster era with plenty of ruthless tackling, compared to the slower tempo of pele's time (though i believe pele would have excelled in any era, class after all is permanent). Also, i dont put that much stock in, the "pele has 3 world cups over diego's 1" argument. team accomplishments imo, is'nt the be all end all in these discussions. why dont we use individual merits as the barometer? it's those kinds of argument that make players like le tissier get overlooked in the grand scheme of things, despite their undeniable quality.
also did pele really play that much of a part in brazils '58 triumph? dont think so. Pele played in a brazil squad burgeoning with supreme talent (jairzinho, tostao etc.....). maradona played with good players as well (guys like burruchaga and valdano had good tournaments too). would argentina have won the '86 tournament without diego? unlikely. would brazil have won '70 without pele? wuite possible. The quality of pele's squad should not be held against him (circumstances afterall), but since you're already splitting hairs in regards to the case of "diego vs. pele", that fact should certainly be taken into account.
at club level look at the disparity between diego and pele. Pele played in the brazilian championship. diego played in Serie A, which at the time was THE gold standard of club football (zico in udinese, platini's juventus, rummenige at inter, the milan dream team of van basten-gullit-rijkard-maldini-baresi-costacurta). napoli won nothing before him and won nothing after him; which is the reason he's god made flesh for those people.
as i said, both are THE GREATEST. You'd be splitting hairs when debating the issue. but it's my opinion that diego has the (slight)edge.