I don't think the masses are Byrd's best music. Increasingly the Motets in the 1605 / 1607 Gradualia are getting more and more of my attention - this is possibly his major masterpiece, or one of them.
Having said that, they've been so little recorded it's hard to tell. I've managed to find a polished recording of music from 1607 from a group called Plus Ultra, but IMO volume 10 of the Cardinall's Musick, which includes a selection of 1605 Gradualia, puts it in the shade, mainly because of the dramatic and passionate performance style. This could well be the best Byrd CD I've heard so far.

It's interesting to compare the style in Cantiones Sacrae with the Gradualia on that disc. The Gradualia are so much more modern, more imaginative, more energetic.
What a shame there doesn't seem to be a complete Gradualia - the project reminds me of Orgelbuchlein and Orgelbuchlein is very satisfying to hear in its entirety, despite not being intended for that. I'm hoping, expecting, the same would be true of the Gradualia.