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.
http://sine.ni.com/apps/we/nioc.vp?cid=1123〈=US
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.