Please post your calculations. I imagine the per capita difference isn't huge. It's probably not "a whole magnitude more."
I know a lot about homelessness. Among other things: I had a class on Homelessness and Public Policy many years ago. More recently, I spent several years homeless. I still blog about it and still talk with homeless individuals regularly.
Your argument doesn't look like a good faith argument to me. It looks like a case of "how to lie with statistics." That makes it difficult to engage with you.
It's not hugely worse. So, the reason it's a whole order of magnitude worse in absolute figures is that New York is a whole order of magnitude larger.
There are probably more accurate figures in New York. California has a really high percentage of rough sleepers compared to New York, in part due to mild temps and dry weather. I have participated in a homeless program that did the annual point in time count. There are serious challenges in counting rough sleepers. You probably see a lot more undercounting of street people than of homeless people using the shelter system. So my guess is the real per capita figures are actually pretty close.
San Francisco has a fairly small footprint and good public transit. It has insanely high housing costs. California has underbuilt housing for decades and has serious systemic problems in that regard.
There is evidence that individuals voluntarily choose to relocate to California while homeless, in part due to the weather. There is also evidence that sometimes other states just issue them a bus ticket to California.
The high cost of housing plus lovely weather contribute to California having more chronic, long term homeless. These people wind up typically being the most visibly homeless. The longer you are on the street, the harder it gets to fit in to normal society for various reasons.
The figures I've seen (some linked above) suggest that California overall seems to have a lot more homeless per capita than the rest of the nation. The most destitute homeless tend to gravitate to the bigger cities because that's where soup kitchens et al are found.