According to the specs, the DVD Navigation system is available as an option
on SE, XLE, and HV (Hybrid) models, regardless of engine. However, neither
you or your dealer is able to order a car from the Toyota factory. Toyota
uses regional distributors (at least one of which are not even owned by
Toyota) which order cars from the factory based on what they think will sell
and they sell them to dealers in their geographic area.  The dealers can
"reserve" a car that the distributor has ordered from Toyota.

Different distributors may have different ideas about whether to build cars
with 4 cyl and Navigation systems. It may also be possible to have a dealer
ask the distributor about ordering some from Toyota, but the lead time for
that is very long, probably longer than you are willing to wait. They may be
reluctant to order one for you because people who can afford a DVD
Navigation system can usually afford (and want) a 6 cyl, and they don't want
to get stuck with car they can't sell in case you back out of the deal.