I guess it would depend what your criteria for "best" is. I presume you mean highest quality rooms since that is the only metric I would give Golden Nugget the highest marks on in the Fremont Area.
I'd probably go with Downtown Grand only because it has the newest refresh - and they have a fun pool area which sets it apart from most of the downtown hotels (G Nugget gets the highest marks for pool too). You can frequently get a suite at many of the 2 star hotels downtown for under $100....The D, 4 Queens, Golden Gate, and El Cortez have nice, cheap suites if you want a little more space and a fridge.