Cleartrip is excellent and professionally run. Very responsive too. They take international cards.

Oher than yatra.com there are - www.makemytrip.com, www.ezeego1.co.in etc

There's also a kayak.com clone called www.ixigo.com - that'll search for fares and then redirect you to the airline's website where you can book. They mark those airlines that take international credit cards (several dont because of the risk of card fraud) with a dollar sign next to the airline (in a box to the left of the screen).