Just south of The Great Highway, there are some good running options in the Lake Merced area that can be stitched together for routes of various lengths and combined with The Great Highway and Golden Gate Park.
Lake Merced Loop. This is a 4.5 mile loop around Lake Merced, mainly on multi-use trails alongside John Muir Dr. & Lake Merced Blvd. Note the path adjacent to busy roads and isn’t right beside the lake, so there aren’t really water views. There’s a ‘measured mile’ for 2 miles on the west side of the lake starting from the southern end.
Fort Funston. Lovely trails around 200 foot high bluffs at the westernmost edge of San Francisco and a great spot to run and watch the hang-gliders! Note: Many of the trails are quite sandy, so the best bet for running is the ~2 mile Sunset Trail, much of which is paved. Combine with Lake Merced, just east, or north on the Great Highway.
San Francisco State University Campus. This urban campus has some nice pedestrian paths for running. Good options are ~1 mile along Font Blvd., which runs diagonally across campus, with Juan Bautista Circle at the center. The main quad is north of Holloway Ave. There’s a running track at the northeast end of campus.