I have a 144hz monitor and figured it would be no problem to run Quake at 144fps, but it appears that it is locked at 60 regardless of the settings in nGlide or the nvidia control panel.

Any ideas what I should try next?
Are there any console commands for that sort of thing?

Turn off vertical sync, that is usually what limits any game to 60 fps. I dont think there is any gain in rendering the game at higher frame rates though. I recommend 'nvidia inspector' as it allows you to set a frame rate limit on your GPU. No reason to cook your computer doing ~900 fps.

cl_maxfps may be the variable you want to play with, but note that allowing super-high framerates can mess with the game physics in most Quake engines (including the original ones). I think a max FPS cap of 77 was the traditional value that folks used.

If you're using ezQuake to play QuakeWorld, there are ways to get higher framerates (if you feel you really need them) as described here: http://wiki.quakeworld.nu/Smooth_Quake and here: http://ezquake.sourceforge.net/docs/?independent-physics

The original FPS cap is 72 and is what is necessary for default physics behaviour. Newer Quake clients implement various commands to adjust the cap with various effects on physics, common commands include cl_maxfps, host_maxfps, r_maxfps. Read the documentation for your client for more information on the exact command and effect.