The better question is: why are you charging them sales tax
at all if they're purchasing your product for resale? That
sort of sale is not a "retail sale" and thus not subject to
NY sales tax; provided, of course, that they've given you
the correct exemption certificate.
However, even if you make a sale that is otherwise a "retail
sale," NY sales tax is not due on that sale if you deliver
the product to a location out-of-state.
If, however, the customer arranges for a third party to
accept the product at your NY place of business and ship it
to the customer (and probably also if the risk of loss
shifts to the customer once you transfer the product to an
independent shipper for delivery, although I haven't
researched this aspect of the question), then the sale is
most likely to be treated as having occurred at your place
of business in NY, in which case it will be subject to NY
sales tax.
For a discussion that is germane to both points above, see
NYS Tax Department Advisory Opinion TSB-A-05(28)S (available
from their website
at:
http://www.tax.state.ny.us/pubs_and_bulls/advisory_opinions/sales_ao.htm).
So, the answer to your question should be: (a) none of the
sales you make to the other NY company are subject to NY
sales tax, provided they give you a proper exemption
certificate, because such sales are not "retail sales," and
(b) any sales that you make where you deliver the product to
the customer out-of-state (e.g., either you directly deliver
it, or you bear the risk of loss until it reaches its
destination if you ship it via a third-party delivery
service) are not subject to NY sales tax in any event,
whether or not they're "retail sales."
However, keep in mind, my remarks are based solely on the
limited facts you've given; please don't do anything rash
and rely solely on my statements without at least checking
out the NY publications on the sales tax, and preferably
without first speaking to your accountant on the basis of
all the facts involved (e.g., what your usual shipping &
delivery process is, who bears the risk of loss and up to
what point, etc...).