Learn English – the meaning of “clocking” in this sentence

I think the existing answers are potentially misleading. It's true that to clock in originally gained currency in the 40s in respect of workers recording the time of starting work (often, in a factory, where they might also clock on, and clock out or clock off when they finished work).

But in recent decades, the specific phrasal verb clock in has acquired another sense. It's now often used to mean record / achieve a "score" in a competition (where OP's "minimum wage comparison" can be seen as a "competition").

This usage is particularly favoured where the "score" values are time-based, but OP's example is by no means uncommon. Another very similar idiom is clock up - to reach a particular number or amount.

Note that the more common phrasing here would be with Rhode Island clocking in at 50 cents higher. In such contexts, to clock in is usually followed by at [the actual recorded value], but in this specific case that would be clumsy - since the actual value is expressed as 50 cents higher at $7.75, we'd have two occurrences of the same preposition in undesirably close proximity.

Having said all that, I agree with other answers/comments making the point that OP's cited usage could (but doesn't have to) be seen as a punning allusion to the factory timekeeping origin of the expression.

Finally, I'll just say that if the writer had used clocking up instead of in, he wouldn't have had to think about whether to follow it with at (which is rarely used after up). But then his pun would be diluted.