Pioto and Josaih are on the right track in suggesting that you should convert the video server-side using a tool like FFMpeg. As far as I know there is zero support for flv in any part of iOS, so you'd be unable to transcode it locally. Even if you could, it would make your users angry, since transcoding is a resource-intensive process that would kill their battery life and take a significant amount of time.
So, your solution is to transcode your videos to h.264 server-side. However, I'd caution against transcoding from flv->h.264 if there are any other options available. If you have the original, uncompressed (or at least less-compressed) source video available, you'll get higher-quality video by transcoding that to h.264. Each time lossy compression (eg, squeeze or h.264) is used on a file, you lose some information and quality. If you've ever seen a 3rd or 4th generation copy of a VHS tape, you can understand what I'm getting at.
Once you have a h.264 formatted video, you can use QTKit to play it on iOS. Not sure about the exact details of QTKit on iOS, but I'm sure it's in there somewhere.