I owned both and can say they are both great basses. I had both of them at the same time so I was really able to A/B them and went with the Geddy. Let me also say that after owning the Geddy Lee for a while I found the neck to be too thin and I swapped it out for a Warmoth neck. I also tried several different pickups and went with a pair of the Nordstrand NJ4. So it is not a GL any more but when I A/B'ed the two they were both stock. Here are a few pros and cons that I found with each that might help.
Geddy Lee
Pros: fairly light weight, looks good, great clarity of notes, simple passive electronics, Badass bridge, 70's pickup spacing
Cons: thin neck caused my hand to cramp up after playing for a while (other players love it though), painted block inlays, tuners were cheap (replaced mine with Hipshot)
Marcus Miller
Pros: active/passive electronics w/ switch, Badass bridge, 70's pickup spacing, true fretboard inlays, very nice slap tone
Cons: very heavy, tuners were cheap (replaced mine with Hipshot)