In Chip 'n Dale, are they male or female chipmunks?

For a long time, there was nothing specific about the two chipmunks to clearly identify their sex within the old cartoons.

From Disney's own site:

Who's Who?

Ever wonder how to tell these 2 chipmunk brothers apart? Chip has a small black nose with 2 teeth in the center of his mouth. Dale has a big red nose and 2 buck teeth with a gap in the middle.

So, if the official line is that they are "brothers", then they must, by definition, both be male.

Historically, it wasn't until the show Chip 'n' Dale: Rescue Rangers that they were ever given clothes or fleshed out personalities. The clothes and personalities are generally male, and there are at least two instances where both of the brothers exhibit an attraction towards female characters.

Tammy the squirrel in Adventures in Squirrelsitting

Foxglove the bat in Good Times, Bat Times

From the Disney Comics Wiki about Chip & Dale:

Their earliest acquaintances were two girlfriends that they both shared, Clarice and Chi-Chi (why they didn't just date one each is unknown).

Also:

They also shared twin nephews, Zip 'n' Zap, and had a common Grandpa (as well as other relatives), which raises the possibility that they are related, perhaps even brothers (they certainly act like siblings).

Plus the page lists them as male in their biobox.

And from Comicvine's entry on Dale:

He is brother to Chip, they are both on the "Rescue Rangers."

And from Magical Mouse Schoolhouse:

According to author Dave Smith in his Disney Trivia from the Vault, Bill Justice, the animator who first drew the rascally chipmunks Chip & Dale, wrote in his autobiography 50 years after the characters were created that he thought of the two as “simply little brothers,” although the Walt Disney Company has never stated if they were brothers or just good friends.

And from the Disneyland* website:

Ever wonder how to tell these 2 chipmunk brothers apart?

(*© Disney, All Rights Reserved, Disney Parks & Travel)

This all seems to point to male.

Just go to the Chip 'n Dale Rescue Rangers wikiquote page and do control-F (or Command-F on a Mac) to search for the word "he" on the page, you can find various lines where the characters were referred to as "he", like this one from Kiwi's Big Adventure:

[When Gadget finds out Dale is faking]

Gadget: Why that little...! He couldn't...! How did...! OOOOH!!

Chip: I know just what you mean.

And this one from To the Rescue: Part V:

Chip: Courage and our friendship binding us together! So follow me! We've got a date with a ruby!

Monty: He's bonkers in the conkers, ya know.

Dale: Yeah? But he is my friend.

(Dale's line here about Chip being his "friend" suggests the writer probably didn't imagine them as brothers at the time, regardless of what the people writing the websites quoted by phantom42 and Meat Trademark thought)