The Sonesta Silicon Valley in Milpitas has rooms at $89 and they have free parking. They are a bit far away, but the VTA is close and they still have rooms with Double/Doubles. They have a link you can use to book.
https://gc.synxis.com/rez.aspx?Hotel=75372&Chain=5157&arrive=5/24/2018&depart=5/25/2018&adult=1&child=0&group=0524FANCON (https://gc.synxis.com/rez.aspx?Hotel=75372&Chain=5157&arrive=5/24/2018&depart=5/25/2018&adult=1&child=0&group=0524FANCON)
They do have some suites with Kings in one room and sofa beds in the other. These rooms have microwaves and little refrigs, but I think are a little more expensive.