Hello;
If the range of frequency would not so extense, you could use one of the NI signal conditioning modules. However, as that is not the case, you will probably need to implement a filter, in Software, to get rid of the harmonics with higher frequency than 100KHz.
Furthermore, I'm attaching a good Application Note that talks about noise on DAQ systems, so you can get some usefull information, and maybe apply some of the techniques on your system to avoid noise.
Hope this helps.
Filipe