Structure with Wish statements about future events: past perfect or past?

The first sentence is certainly more standard. Traditionally, the word wish, in English, took a verb in the subjunctive mood after it. To express something in the future, the past subjunctive was used.

In your example, the indicative is used (wasn't), rather than the subjunctive (weren't). Using the subjunctive, your sentence would read:

The weekend has flown by; I wish it weren't Monday tomorrow.

However, as the subjunctive's use became progressively less (see this discussion), the indicative came to be used in it's place progressively more. It thus became common to use the simple past (indicative) to express the future in hypothetical and non-actual situations, as was done in your first example.

In summary, it's more standard to use the past (whether indicative or subjunctive) to express the future after wish.