If you are in NYC or other large Jewish communities there are many reputable (and many otherwise, so be careful) soferim who can sell kosher tefillin at any level of hiddur. If not, a number of reputable soferim have websites and will ship. I recommend the following:
Eichlers.com (not a sofer, but they are the major judaica retailer)
Hasofer.com (a mostly online retailer. They have a large selection of tefillin)
ajudaica.com (online retailer. Do not buy the low-end bar mitzvah set. They are rarely lechatchila and I would only recommend them for people who genuinely can’t afford an unquestionably kosher set.)
Google around and you can find a few others. Tefillin are a big ticket item and you should shop carefully, inspecting in person if at all possible. If you have any specific questions, post them here. There are a couple soferim on the forum plus many other very learned people.