Contractors 3 weeks overdue on rehab - what to do?

[David Hald]

Hello Everyone,

In early December, I bought my first property, a Midwest duplex in a mid-size city. 

It needed a refresher, so I got some bids, and hired a contractor/company, who also does snow removal/lawn care. They gave me an estimated finish date of January 5, 2019.

Some work has been added by me, as the process has progressed, and some delays have been incurred due to my distant location (I'm working in Asia) and starting up a new job with training et. al. here. 

However, on the contractor's end, it seems they literally stop working depending on the weather, since they are primarily a snow removal company. The fact stands that it's now 3 weeks after their estimated finish date, and they still aren't done, although not much remains to finish the house. 

As you can all gather, I have some empathy for their situation, but this delay is costing my hundreds per month in holding costs. I put in a condition in our Independent Contractor's Agreement for a 1% per-day-overage-fee past the estimated finish date, but I am hesitant to bring that up, since these guys still have to finish the job, and I may want to hire them again in the future. Should I simply pay them the reduced amount after they finish? Should I try to negotiate now? After they finish?

What would you all do?

Thanks in advance!