The Waterfront Plaza Hotel is one of my favorites. If you select a waterfront view with balcony, you get a nice look at the estuary which is very calming. Their service is good and rooms are always very clean. I've stayed at this hotel about four times. As a woman, I feel safe in the hotel and there are many, many amenities if you want to enjoy the wonderful nightlife in a hassle-free way.
The hotel is in Jack London Square which includes several great restaurants including Scott's seafood that has a fantastic piano bar and delicious high-quality meals. The hotel itself has a lovely French-style bistro, the best jazz club in the country, Yoshi's, with outstanding performances seven days a week (Yoshi's is also a 5star Japanese restaurant).
You are steps away from a 4-plex movie theater, shopping, an outdoor market on the weekends, and if you're lucky enough to be in town on a weekend when there's a festival, your hotel is right in the middle of the action. This is the perfect hotel for the Fourth of July as you can sit on your balcony and enjoy the festivities from a perfect location. The hotel is in walking distance to downtown and Lake Merritt.
It is true that the Amtrak station is nearby, but the sound of the trains is not obnoxious. For me , the trains lull me to sleep and is a very peaceful sound. Also, in the morning are the seagulls and again, not overbearing, just a nice wake up call. I adore this hotel.