The "nicest" hotel that meets your criteria is, in my opinion, the Parc 55. Note that as a diamond you'll need to kick in $10 for hot breakfast (which is high quality). As a diamond you will likely be upgraded to a high floor with a good view. This property is literally across the street from the Powell BART station and in case you want to walk around downtown at all, it's still a relatively active area even around 10PM.

Practically speaking, in your situation, I would personally stay at the Hilton Oakland Airport. Last time I stayed there it had a free hot breakfast which was OK. The rooms are not "nice" as it's pretty dated. The reason I am suggesting this property is that it takes BART out of the equation in the morning. A small earthquake or other disruption that interrupts BART service could mean a missed flight for you in the morning. Note, I'm more risk-averse than the average person and have not ever personally experienced significant interruptions of this nature.