It was a number of years ago, but I enjoyed several days in Kyoto at the New Miyako hotel, almost across the street from Kyoto station, which I considered very good value for the price. It's a very good full service hotel though perhaps not in the top luxury category. (Note: this is a different hotel from the Miyako, located elsewhere in Kyoto.) It's true that the neighborhood is dreary -- this neighborhood was the model for the future LA in Blade Runner and it looks it, especially if it's drizzling all the time like it was when I was there. But I found it perfectly safe, and unless you have a car it's extremely convenient to be right near the station, since you'll be going there a lot to take trains or buses to Kyoto's spread-out attractions.

Travel tip: Kyoto station is huge and confusing, and if you're not familiar with it you should allow plenty of time to catch your train. It's so big that even if you know your way around it can still take ten minutes to get from the station's front door to your platform, if I remember correctly.