It may have been "very active" but it was a small part of the overall scene. I lived up and down the peninsula throughout the dotcom boom. SF was on the periphery of tech during the 1990s, the major migration up there happened in the years after the bust.
(Caveat: I'm thinking of the 1997-2000 period. Netscape IPOed in mid 1995, the bust was early 2000, so that covers the last 2/3rds of the first wave, but not all of it.)
My observations at the time: dotcom-1.0 was split pretty evenly between SF and SV, but there were clear differences in focus. Hardware and legacy stuff was all in SV, software/web/media was substantially all in SF.
Dotcom-2.0 (social media/SaaS/etc) was entirely in SF.
I'd agree that SF owned 2.0 and shared 1.0, but 1.0 in the city was extremely busy with founders, employees, launches, leases, and money.
I worked up and down the peninsula. Investors and data centers (VCs and DCs) were down south -- the latter with one exception: 200 Paul Ave, although itself at the extreme southern edge of SF.
Founders, staff, offices, and everything else were in the city.
I worked at one company who opened an office in the valley, but we literally couldn't hire people down there (Santa Clara), and couldn't get people to move there. All the action was in SF, for a software/web/media business.
While dotcom was obviously lots of companies, the big three were Netscape (client and server software), Sun (servers) and Cisco (networking). All three located within a stone's throw of each other in Mountain View-Sunnyvale. I worked at two of the three, and spent a lot of time hanging out in the third.
There was nothing of note up in SF in those days. SF was the place to go up to party, but no known companies existed there. Everyone I knew who lived in SF would commute down to Silicon Valley in the 90s.
After the dotcom bust, when tech morphed away from actual tech and into social media, SF became a hotspot. But that was several years later after the crash.
That's funny, because I also worked at two of those three, and I have a distinctly different memory.
NSCP, SUNW, and CSCO did not in any way define dotcom-1.0. Except maybe in the national press (Fortune, WSJ, etc). They were important parts, but not particularly special on any axis: money, employees, technology, cachet.
NSCP IPO was a defining moment, but the corporation was ultimately nothing in the boom. CSCO and SUNW were not even startups, they just produced higher volumes of their (mostly) existing product lines.
Obviously we're coming from different frames of reference, but I stick to my assertion. SF city was crawling with startups, startup money, and startup employees. So was SV.
I certainly can't deny your experience but sure it's different.
All the hype and money and "cachet" was in Silicon Valley during dot.com boom.
Having been deeply embedded in that era of Silicon Valley, I can't think of a single recognizable tech company in SF in those days. Later, absolutely. But not in the late 90s boom.
Netscape IPO kicked it off and Sun and Cisco took it to the heights now known as the dot.com boom.