My best advice for anyone applying to residency is don't worry about salary anywhere. It's irrelevant.
In Harbor's case, there's a reason why the intern salary is so low. There are large transitional year and prelim programs that are very competitive because of the location. The hospital doesn't need to pay competitve intern salaries because so many people want to be in the South Bay area. The 44k base salary is for all interns, but those who stay on as second years as part of a categorical program get an automatic 2k bonus. Additionally, the hospital gives residents 3 meals per day, which ends up being thousands of dollars in savings compared to other programs where you buy your own food. Finally, the benefits really are incredible at Harbor. You get an allowance for health insurance that is generally worth more than the price of any insurance program, and the hospital pays you the difference. So, for example, Harbor covers my wife and I, and also pays me $240 per month because I'm under the allowance. That's another 2500-3k per year above your salary. As a final point, Harbor has had many residents with multiple kids who are single-income families, and they have been able to find good housing in one of the countries best cities.
Every hospital is unique. Salary shouldn't be a consideration in choosing a program. Choose the program you like best and best fits you. One or two thousand dollars today is chump change compared to what you will be earning as an attending.