I guess there are 2 outputs with 90 degree phase difference. If so, you need to sample the 2 signal and calculate the instantaneous phase continuously, with buffered AI. By calculating the phase change per second, you get the speed
Sounds like what you have is a resolver, not an encoder. For hardware to decode a resolver, you can try Helm Instrumets, in Maumee, OH., or Toledo Instruments (not Toledo Scale). Their web sites will show what you need.
Our 6602 counter/timer boards are perfectly suited to encoder and position measurements. They come with eight 32 bit counters. They also support buffered counter operations.
If you wish to do more than just counting with your board, I would suggest one of our new M-series DAQ boards. They come with 2 counters and support buffered counter operations. They also have the functionality to take quadrature encoder and position measurements.