It depends on what you're looking for.
Onsite?
Disneyland Hotel all the way. Nice, quiet, spacious rooms, extremely clean, extremely kind staff.
-Grand Californian isn't worth the cost IMO. Too many use it as a midday break in the lobby, the hallways are long, the rooms are smaller. It's a great hotel, just not worth $800+/night. OTOH, Disneyland Hotel is very much worth paying $950+/night for Club Level. Highly recommend Club Level if you can swing it for the DLH.
-Would not recommend Pixar Pier Hotel/Paradise Pier (not sure if it has fully changed over). Relatives stayed there about 5 years ago and a big negative is the elevator being slow/always full and the rooms being too small.
Offsite? There is a wide range of available hotels/motels/inns along Harbor. My recommendation from a convenience/safety standpoint is to stay on Harbor in between the borders of Katella and Ball. Plenty of less inexpensive all the way to moderate options.
These are the motels I would recommend. All are clean, safe, comfortable. We've stayed in all of these within the past 6 years. Listed in order of recommendations:
1. Desert Inn and Suites (free breakfast)
2. Camelot Inn and Suites (recently refurbished, within the last few years)
3. Tropicana Inn and Suites (sister property of Camelot, also refurbished recently and has a nice convenience store attached for water/soda/beer/wine/snacks)
4. Del Sol Inn
Moderate:
1. Courtyard Marriott Theme Park Entrance
2. Desert Palms (free breakfast)
Ones I would not fully recommend based on our experience in the past 5-7 years:
1. Hyatt House at Anaheim Resort/Convention Center (noisy, thin walls)
Others that are available that seem to get good reviews but we don't have experience:
1. Candy Cane Inn ****this one just reopened after an extensive refurbishment and had many issues with postponing the date of reopening, but so far it looks great and it has a shuttle.
2. Fairfield Inn (we stayed in this one when I was probably 4-5 years old, so 20 years ago. I haven't heard anything bad about them but can't give a review based on anything recent)
3. Howard Johnson (this one usually gets very good reviews)
4. Grand Legacy (rooms in the newer building can have noise issues based on the rooftop bar, other buildings are further away in property)
5. Anaheim Inn (recently refurbished within past few years, haven't stayed there since)