We will be ending a cruise in San Antonio, Chile the first week in January. We are debating flying to Cusco and spending a week seeing Cusco, Sacred Valley and MP. We know it's the height of rainy season so have mixed emotions as we are not sure we would come back to see MP. If we go we would spend 2 nights in MP to have 3 days to see if one is very rainy. Anyone been there in January? TY

I have been in Cusco and the Sacred Valley in January and it can get very wet. Expect frequent showers and occasionally heavy rain, especially in the afternoons. To maximise your chances of decent views at Machu Picchu, avoid early mornings when mist often blocks the views. That said, being the rainy season, accommodation prices are lower and everywhere will be green so, if you do get some sunshine, the views will be amazing!

I appreciate the desire to maximise the opportunities for decent wether at MP but bear in mind that you will stay in Aguas Calientes which is not the most enchanting place in which to spend time. Most people will just visit for the one night, see MP and get out. Ollantaytambo is a much nice place to stay but that involves a two hour train ride each way so not viable for a 2/3 night stay.

Bear in mind that it is not just a question of booking 2/3 nights near MP you need to allow time to get there. i.e. fly Lima to Cusco(1 hour ++), taxi to Ollantaytambo (2 hours) (overnight stay would be needed). Train to Aguas Calientes (2 hours) , bus to MP (1 hours). You would also need to get back! I cant imagine visiting MP and not spending time in Cusco , ideally a couple of days. Essentially , I think you would need to allow a min of 5 nights in total .

I think we will chance rain and plan 2 nights 3 days in AC to maximize days in MP due to rain. Good advice for afternoon vs mornings. We do plan 7-8 days for total trip to sacred valley, Cusco and MP. Thank you

Be sure to give yourselves time to adjust to altitude!

If you haven't already seen it, you might find some useful information in my trip report:
Praise for Peru – A report of my solo month in this amazing country
The section on Cusco and the Sacred Valley begins with post # 91.

7-8 days is a perfect amount of time to cover Cusco and the SV.

Coming from sea level, I would ideally put your stay in Aguas Calientes/MP at the beginning as they are at a much lower altitude than Cusco and you will acclimatise much easier. I would plan your flight from Lima in the morning to give you time to get to Ollantaytambo , spend the night there and head to AC the following morning.
Even though it is the low season, I would book your train tickets and entrance tickets in plenty of time as they could still get booked out and you need to choose your routes around MP . Use only the official sites.

I could have traveled in December-January but I planned my trip for June to July to minimize the chances of rainstorms. For Machu Picchu I am spending two nights in Ollantaytambo, taking a day trip by train and bus, entering the site at 1pm. Yeah I know some people prefer the idea of staying in a hotel in Aguas Calientes (Machu Picchu pueblo) the night before and then arriving at the ruins of Machu Picchu at sunrise or shortly after. Maybe your cruise is enough for one trip. Can you plan a separate trip to Peru?