In September, my husband and I will be in San Francisco and plan to catch the Coast Starlight heading north. Their website shows several departure points from which to catch the bus to Emeryville to catch the train at approx. 10:00 pm. Buses leave at approx 9:00 pm. from several locations in San Francisco: Ferry Building, Fisherman's Wharf, Peninsula Line, Union Square.

My question is which would be the least creepy at that time of night? We may be closest to Union Square but I don't mind taking a cab to another location. Also, does anyone know if there is a place to store luggage, or should we try to keep at the hotel we will have checked out of that day?

Do mean "creepy" as in something you haven't experienced before and are somehow afraid of or "creepy" as in slow? I think these places for boarding the bus are simply boarding points and don't necessarily offer any other services (such as at the Ferry Building.
You might be wiser to store your luggage at the hotel. You could, theoretically take a taxi all the way to the station, too.

An alternative is to spend the afternoon/evening at Jack London Square in Oakland at catch the Coast Starlight there (Oakland is the AMTRAK stop just prior to Emeryville). The AMTRAK station is at the south end of the Square.

There are museums, shops, and over a dozen restaurants (my favorite is Scott's Seafood) in the square.

A fun way to get there is the Oakland/Alameda ferry which you can catch at either Pier 39 or the Ferry Builing. Going over in late afternoon might be more comfortable for you than catching the AMTRAK bus after dark.
The ferry lands at Jack London Square and I suspect you would be able to check your luggage in with AMTRAK when you got there so you would not have to carry it around.

dowooddon has given you a great suggestion. It would let you visit a really terrific area of shops, restaurants and waterfront sights and be right at the train station. Would be a lot easier and more fun that trying to rush across the bay on public transit.

Sorry to be so vague there, Intrepid. I meant creepy as in feeling unsafe - which I have experienced before but would rather avoid.

Thanks for the suggestion, dwooddon! I had no idea about this option. Will definitely look into this. And thanks janis for seconding the idea.

I don't think any of the locations mentioned are exceptionally creepy (though I've never heard to Peninsula Line). The Ferry Building, Wharf, and Union Square will all be populated with other tourists and folks during those times.

The Ferry Building is right near two very busy great restaurants, One Market and Boulevard.

Union Square is always filled with shoppers, and Fisherman's Wharf is tourist central.

Ok, good to know, SFImporter. Let me know if you have any other restaurant suggestions. I'm looking forward to at least one dinner at a waterfront location with a fabulous/romantic view. We like rather basic, non-garlicky food preferably not of the artfully-arranged-in-the-middle-of-the-plate variety, if you know what I mean.