What's a better choice? Manley Steelhead Phono or Audio Research Reference 2SE Phono?

You may get more system symmetry with the Ref2 SE.

Agree with system synergy - either way get them under top grade HRS isolation 

I've had the ARC Ref 2SE for a couple of years now and its a magnificent phonostage. The ARC Ref 2SE has balanced output, which if all things equal, I would chose over a phono preamp with only single ended outputs.  That's a personal choice based on my experience.

I have ARC gear (Ref 6 and Ref 150SE) and the Steelhead, all bought new. I love the sound I am getting and love the Steelhead. Where I can't help you is that I have never tried the Ref 2SE. The Steelhead has an outboard PSU but that alone means little. Both have two sets of RCA inputs to enable having two tables hooked up at once (which I have). The Steelhead combines circuit-derived gain for MC with autoformers, the ARC does not, but again, that means little. I would think adjusting gain and loading is easier with the Steelhead. I suspect you can't go wrong with either. I believe in system synergy when matching an amp and preamp but don't think it extends-to the same extent (pun)-to matching a phono stage. Bottom line-you can't go wrong with either. 
rdk777 makes a great point about the balanced output. I would prefer that too.