Probably the best aftermarket air intake filter for the stock closed element intake would be the TRD one, if they make one. A K&N would come in at a close second. AFE may make one, they make for most import intake kits, AEM, SRT, Blitz, Greddy, etc.
Doubt you see significant gains if any, maybe a deeper audible growl, single digit percentage of mpg increase obviously depending on how you drive.
Bear in mind most aftermarket air filters are reusable or rechargable. Which essentially means that you have to clean and re-oil the filter yourself.
These oil-type filters get dirty much more quickly than paper filters and depending if you apply or comes applied with too much oil, that can get on the MAF sensor within your intake that will negatively affect performance and gas mileage. These type of filter require much more maintenance than normal, at least cleaned/checked every other oil change to achieve optimal performance out of this mod.
Rule of thumb is to clean the MAF sensor with electric cleaner a few days AFTER you recharged your aftermarket filter.
In my experience a 30, 50, $70 aftermarket filter just to replace a paper one does not do much. Unless you plan to replace the entire intake tubing, an aftermarket filter for the ram/cold/open intake would then be beneficial. Don't know of anyone that makes intakes for the Highlander, but I would assume ones for the camry or avalon or rx330 may work. If anyone makes kits for the v6's for those cars even...
[edit]Didn't find anything on the carson toyota site, but found something here:
http://www.brandsport.com/performance168.html Never heard nor used them before though.[/edit]