It's a relatively new model from Marantz, so it's not surprising that review information is hard to come by. Marantz hardly makes garbage and the SR4001 should be more than acceptable.
From the Marantz SR4001 to the Onkyo TX-SR674 you would gain HDMI up-conversion (convenient), audio delay (especially important with certain TVs), a per-speaker adjustable crossover with sub-80 Hz options, and some sort of iPod compatibility (the specifics I don't know) and lose the speaker pre-outs (but the sub pre-out remains; the former are required to use an external amplifier) and HDCD decoding (most people don't know or care about HDCD decoding).
To the Yamaha HTR-5990 you'd gain HDMI up-conversion, audio delay, and a third zone and lose the HDCD decoding. I'm pretty sure the Yamaha offers a couple sub-80 Hz crossover options over the Marantz, but they won't let me download their manual to double-check with nagging me to register.
Onkyo and especially Yamaha are known for offering more DSP modes than Marantz (which has a more "classic approach" reputation still). Personally, I find Marantz equipment very pleasing to the eyes and this particular Yamaha rather unattractive (the Onkyo falling in the middle).
