'99 Toyota Sienna intermittent missing

Can you confirm that the code is always a cylinder 3 misfire (P0303)? If it is that means one thing. But if it jumps around from cylinder to cylinder or goes to a multiple/random misfire (P0300) that would suggest other things.

If it is ALWAYS cylinder 3 then I would suspect a fuel injector and maybe swap #3 with another.

But in the midst of pulling apart the fuel rail, I’d pull the plugs back out at check the compression - obviously looking to see if cylinder 3 looks much different from the others. So I’d extend the list from bloody_knuckles to four things. To get combustion in there you need gas and air and compression and spark. For a single cylinder misfire that remains with that cylinder the top possibilities are the fuel, spark & compression.