@SqueamishOssifrage has given an accepted answer, so I assume that it addresses your concerns. However the question as stated was about randomness tests, and I think there's something to add concerning that aspect of the question.
I am more familiar with the TestU01 than NIST tests, but based on what I've read in Johnston's Random Number Generators--Principles and Practices, I believe that the following is true for at least most of the NIST SP800-22 tests as well.
These are tests such that, if your numbers were generated by a series of independent uniformly distributed random variables--which is what I take a uniformly distributed TRNG to be supposed to produce--then it would be very improbable that the set of numbers would exhibit the patterns that these tests look for. That is why the tests are based on p-values: A small p-value for a test means that the test is detecting a pattern that would be very improbable if the numbers were generated by a uniformly distributed TRNG, providing evidence that the numbers are not like those that would be expected from such a TRNG.
Your problem is that you believe that the numbers are unlike those produced by a TRNG in that duplicates have been removed--or at least you hope that they have been.
(Ruggero's question in comments and Squeamish Ossifrage's comments about the size of the numbers is relevant here. If they were 16-bit numbers, for example, then given the size of your set, you would be guaranteed to have duplicates.)
So, in theory, you could take each test in the NIST suite or TestU01, and work out what patterns would be improbable on the assumption that duplicates have been removed, using this to construct new tests. Then apply your alternative tests to the numbers. This would require some statistical reasoning and hopefully not a lot of extra coding. TAOCP volume 2, chapter 3 would be a good starting point. It's old, and there are additional tests in the recent test suites (with smaller p-values required for failure, I believe). However, Knuth walks you through the reasoning processes for constructing these tests and provides a semi-cookbook/semi-theoretical introduction to the relevant statistical methodology.
Alternatively, given the size of your numbers and the size of the set, maybe it is possible to prove that the tests in the test suites would not be very sensitive to the presence or absence of a few duplicates. In that case, you could use the test suites as is, and use a separate duplicate-finding algorithm to test for uniqueness, as Squeamish Ossifrage suggested.
EDIT: Another option would be to add back duplicates, and then run the NIST or TestU01 suites. This is not as crazy as it might sound. On the assumption that the generation process is uniform and independent for each number produced, there is a probability distribution over numbers of duplicates (given the size of the set and the number of bits in the numbers). You might want to test for duplicates first, but if there are none, then you can use a sampling method to add them back with probabilities equal to the probabilities of their appearance in the first place. I know of at least one scientific paper that had to do something roughly analogous to this in order to apply statistical tests that the authors had designed. (I'll add the citation if anyone's interested, but it's far from cryptography, and finding the relevant part of the paper and understanding what they're doing requires some explanation.)
ANOTHER EDIT: @SqueamishOssifrage's comments made me realize that I should emphasize that PRNG test suites like TestU01, NIST SP800-22, or Dieharder were originally designed for people developing PRNGs. They may be designed to be easy to use, but it would be worth at least skimming the background documentation for TestU01. Implicit in my statements above about what is probable or improbable is that the improbable can happen. That is, one can get a test "failure" even if the set of numbers being tested should be considered OK, because it is only probable that a good set of numbers will pass each test. If you can test lots of numbers, this is less likely, but it's still possible. (However, I believe that by default TestU01 uses very small p-values such as $10^{-10}$ as standards for failure. That is, failure means that your data has patterns in it that would only have a 1/10000000000 chance of occurring if it had been generated by a truly uniformly distributed generator. On the other hand, there are multiple tests in TestU01, so your data gets multiple chances to exceed this limit. But it is an extreme limit nonetheless.)