I prefer JUnit assertions as they offer a richer API than the built-in assert statement and, more importantly do not need to be explicitly enabled unlike assert, which requires the -ea JVM argument.
In JUnit4 the exception (actually Error) thrown by a JUnit assert is the same as the error thrown by the java assert keyword (AssertionError), so it is exactly the same as assertTrue and other than the stack trace you couldn't tell the difference.
That being said, asserts have to run with a special flag in the JVM, causing many tests to appear to pass just because someone forgot to configure the system with that flag when the JUnit tests were run - not good.
In general, because of this, I would argue that using the JUnit assertTrue is the better practice, because it guarantees the test is run, ensures consistency (you sometimes use assertThat or other asserts that are not a java keyword) and if the behavior of JUnit asserts should change in the future (such as hooking into some kind of filter or other future JUnit feature) your code will be able to leverage that.
The real purpose of the assert keyword in java is to be able to turn it off without runtime penalty. That doesn't apply to unit tests.
This may not apply if you exclusively use stuff that's shiny and new, but assert was not introduced into Java until 1.4SE. Therefore, if you must work in an environment with older technology, you may lean towards JUnit for compatibility reasons.
I'd say use JUnit asserts in test cases, and use java's assert in the code. In other words, real code shall never have JUnit dependencies, as obvious, and if it's a test, it should use the JUnit variations of it, never the assert.