Unfortunately the answer depends a little bit.
For the longer term having the blog and store all in one place under one domain makes the most sense.
This also makes sense for SEO, as the blog will help the store to rank better if optimized properly.
However, in order to accomplish this you may run into some short term issues.
If you do move it, make sure that all URLs are mapped and 301 redirected to the new URL. This will minimize any disruption.
What happens depends on how much content there is and how many links there are.
For example - say your word press blog has 10 links and 1000 pages, redirecting that to the store and adding 1000 pages will likely dilute your page rank and will probably make it rank lower in the short term.
Another example - say you have 100 links and 100 pages, redirecting this to the store would probably be OK.
Another option would be to do it in stages. If there are specific sections that can be redirected first that would be good.
The next thing I would do would be to start producing the content on the main store site. Then I would look at which blog posts on the WordPress site have the most links and get the most traffic and move and 301 redirect those to the store.
So, the best option does depend on the specific situation. There are many options and ways to achieve this. If this is a long term business moving it is probably better than having it separate.