Is there a problem with using the WAV format for non-audio signals?
I think WAV will be a good format for your data as it supports:


Integer Hz sampling frequencies (like your 1000 Hz).
Integer sample formats (like 16-bit, 24-bit, 32-bit).
A floating point sample format (32-bit IEEE float).
Multiple channels.
Seeking (quickly reading the file at a specific time point in the audio).


Other nice things about WAV:


You can use FLAC to compress WAV files for storage and transfer.
WAV files can also contain non-PCM data (such as markers and metadata).