I would use TTLS unless I had a reason not to. It's tried technology and supported across more platforms.
Here is a good (if somewhat long) overview over at O'Reilly. Be sure to read the comments to the article for more opinions.
Here is a quote from the conclusion
Though there is not a large technical difference between the TTLS and PEAP protocols, TTLS has a number of slight advantages. In addition to a slight degree of flexibility at the protocol level, products are available now and support a much wider variety of client operating systems.