First time visit.
Taking 2.5 weeks for honeymoon in mid May early June. We are thinking of S.F and Lake Tahoe. We are renting a flat in SF and a place in Tahoe. With many day trips planned.
But want to get the hometown experience as well. The locals restaurants and parks, not just the tourists haunts...plan on taking the Muir Woods tour/Alcatraz but not many plans after that. Is the Japantown/Golden gate Park area a nice place to rent?
Thanks for reading this lengthy post...

Do you mean Japantown or GGPark area, because these are two separate areas? If you have a more specific location, the SF locals will be more than happy to give advice.

We recently stayed in Japantown. It was perfect! We were near Haight Asbury, Pacific Heights and were able to get to Union Square and walk from there to Chinatown, Northbeach, etc.
We love San Francisco and were very happy with Japantown.

Thinking of the area between JapanTown and GGpark - is this Western Addition?
Can you tell which intersection - it may be not the area advised to tourists.

If you are going to rent an apt in SF for a holiday, check the listings on craigslist.org. Under "housing" they have a posting area for vacation rentals. Some parts of the area that you are describing would be as safe as anywhere else in SF. There is also a small hotel on the border of GG Park called the Stanyan Park Hotel. The location might work for you.