Obviously, you can't use the word "cook" sushi since it is served raw (in most cases).
What other verbs can I use to describe the action aside from make and prepare?
She __ a whole tray of sushi yesterday.
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Firstly, it's very much worth noting that sushi is actually rice. Although it's sometimes served with raw fish (which is sashimi), it's a separate thing, with the rice prepared with vinegar (or with a kind of vinegar-powder that approaches chemical-weapon status if you happen to breathe it in by mistake).
That said, I would go with any number of options. For the sushi itself, it'd be rolled and cut – and for raw fish, it'd be sliced, prepared, or arranged, I think, though I'd personally lean away from using any of them. My inclination would be to describe the result, something like:
"She emerged carrying a tray of sashimi, the slices arranged as flower-petals around circles of daikon."
– versus –
"She'd tried her hand at sashimi, but had ended up with a tray of ragged chunks, far from the delicate slices on display in Japanese restaurants."
Of course, neither might be appropriate if you're writing a factual article, but for fiction, I think these approaches offer something more colorful about the person who's doing the work.
Sliced or chopped, perhaps? Note: If you choose one of these, you must change the sentence.
She sliced sushi and put it on a tray yesterday.
She chopped sushi and put it on a tray yesterday yesterday.
If you're looking for something like "prepare", then
She arranged a tray of sushi yesterday.
(This one sounds the best to me, but everyone's opinion differs...)