In broad terms you have three options: (1) as you suggest, try to change the regulation itself, (2) try to get the zoning definition changes OR (3) try to get a waiver or exemption
to the zoning for your particular business.
1. requires you to go to the municipal town council and petition for the change -- this is, in effect, a political process and you'll need to gather support in the community for the change. Taking this approach from a legal standpoint -- meaning, attacking its viability in the courts -- is possible but you would need to prove that its application somehow impedes an inherent right OR that it unfairly targets you. Not necessarily an easy approach.
2. requires working with the planning board for the town -- hopefully there isn't a huge outcry against your business (and hopefully the reverse is true, or you can garner community support for your business in that location) -- but it would require an application to have the zoning definition for the particular unit/building amended to an appropriate one (though, if the 1000 foot regulation still prevents you from moving in, you'll still have to go with 1 or 3).
I would suggest to you that 3 is your best avenue for success. This would require bringing both the municipal government and planning board in and having them okay your particular business in that particular spot despite both the zoning and 1000 foot regulation. Again, the value of community support cannot be understated here, so getting other local (and surrounding) businesses to support your petition can be very helpful.
With all three approaches a good municipal lawyer is invaluable since they'll not only know the proceedure preferred by your local municipality BUT they'll have insight into the particular proclivities of both planning board and municipal government when it comes to allowing variations of this nature for businesses. You definitely want someone local that's experienced in these matters since that experience will likely be what makes the processes smooth(er) (as unfortunately local politics of this nature can be extremely rough to navigate)
To get in touch with a local lawyer who can help with this, see: LINK
Regards XXXXX XXXXX best of luck.