We're using 1920x1080 at 29.97fps for our mp4's is there a different format that would "work better?"

If you have 1080p displays and your computer is capable of projecting at that resolution that would be fine. 720p (1280 x 720) MP4 is another excellent option, especially for older, less powerful computers. Essentially you need to match your media to your computers capabilities.

Also, watch your bitrate as that will have a major impact on how well they project. If the bitrate is too high, such as the videos created on Macs using iMovie or Final Cut. Those two programs create video files with extremely high bitrates that far exceed what are needed.

And EasyWorship will display any resolution, bitrate, fps, etc. How well they project/display is completely dependent on your hardware (computer).