What is the best way to obtain permits hauling commodities?

If I was going to pay someone to do that I would more than likely use www.ooida.com

 

Oversize & Overweight Load Permits - U.S. and Canada - WCS Permits

Keep in mind, if you are talking about trip and fuel permits to take your local trucks across the state line you are limited to only a few trips per truck per year before you must obtain a IFTA and IRP account. Also trip and fuel permits are not cheap, each permit is $73 to the Commonwealth of Pennsylvania and between $25-$40 to the issuing service (depending on who you use). I can't recall if in PA the trip permit covers both IRP and IFTA or if a separate IRP permit is also required. Even though these permits are good for 5 days they are single trip into or through the state so you would need a new permit each trip from NY into PA.

Now, if you are talking about weight permits for loads over 80,000 gross (like the NY R permit) Pennsylvania doesn't offer divisible load weight permits (to the best of my memory) so your gross would be limited to 80,000 on a 5 axle combination and 73,280 on a 4 axle straight truck.

It may be best to put apportioned registration on the one truck you plan to go interstate with and get an IFTA account. PA doesn't have any other special permits like HUT so your compliance is fairly simple. Don't forget about ELDs for the interstate trip if you are outside your short haul exemption and not otherwise exempted from ELD due to model year.