Mt Hamilton is a long climb, not hard just long. The east side is very remote. No services or water till you get to the Junction, then down Del Puerto there's water at the county OHV park. Once you get to the central valley you have to go north, which is usually into the wind.
Niles sucks for riding. Narrow, no shoulder, fast traffic. If you do it, do it early. You can go north on Palomares, which is about a 1000' climb, to dublin blvd.
The easiest would be Calaveras and Patterson. There's a climb up Calaveras and a "wall" when you make the left turn but it's short. Patterson going east is also a short climb and a great descent. You can get water and food in Sunol, Pleasanton and Livermore. I think it's vinyard which is the good route from Pleasanton to Livermore.