Hi,
You haven't said if the site is for you or a client, but I usually ask the client for a list of keywords for their industry. Interestingly, these aren't necessarily the best keywords to use, as either some really obvious ones get left off, or they are so into "industry speak" that they forget what the ordinary man on the street would use to find them.
from there I would put that list of words into the google keywords planner tool. https://adwords.google.com/KeywordPlanner
You could do with giving us more info though. Is this site local, or national, or international? That will determine how you use the tool.
Regardless, put in the keywords and "search for new key words and ad group ideas". From there you hopefully will end up with approx 800 keywords to start to work on. You can usually cut this down in half immediately as many of those words will be of little value.
As an alternative, go find your competitors web pages and see what keywords they are using (sometimes if they are dumb enough, they will have written them into the site - inspect the back end of the code by right clicking on the page and view page source).
Last thing I will say is if this don't scrimp on time allotted to keyword research. It's absolutely imperative that you get this right at this stage, as it will set the direction for how the website will look, and how you will run the site. My opinion is that the best keyword research brings the best results. I usually spend a couple of days (16 - 20 hours) at least before embarking on a new site.