As a general statement, since the data is required under the authority of an NPDES permit, it must meet the same standards as the municipal WWTP for it's NPDES, as described in Part II.B. These same requirements are also in the Part 23 Rules, R 323.2309 (6)(c) and (d). That means that they have to use EPA-approved test methods (40 CFR Part 136) and have a QA/QC program that includes equipment calibration. The same recordkeeping requirements apply.
Further, under the Clean Water Act and regulations, 40 CFR Part 122.41(e) requires permit holders to "operate and maintain all facilities and system of control..." and states that "proper operation and maintenance also includes adequate laboratory controls and appropriate quality assurance procedures."
There is nothing wrong with having an in-house laboratory, but they have to have the same QA/QC requirements as a contract laboratory if the samples are to be used for compliance purposes.