My position is ending because of grant funding, I've been there three months how do I convey that on a resume

Is the best way to convey that in the cover letter?

You should save space in your cover letter for more relevant things. I think it's better to talk about the relevant experiences you gained in during that time rather than talk about why it was a shorter term.

On the resume I could put an end date instead of present. What do you guys think?

I think keeping it as 'Present' would be better. The situation hasn't been set in stone yet. If people ask why you're looking for a new job, explain to them the funding situation. You're not doing anything wrong, you're just looking for opportunities in case things turn bad.

In the case where they end up not renewing the funding, you might want to update your resume to contain something like what @Joe Strazzere said in the comments:

Research Assistant | Winter - Spring 2019 - Funding Not Renewed

I personally think it isn't that important to point out why it was a shorter term. I'd rather let the experience speak out for itself and try to put more emphasis on that.

Something like this:

Research Assistant | Winter - Spring 2019

Operated So & So,

Conducted This & That

This way, when potential employers look at your resume they'll see the experience you bring to the table, not the lack of experience due to the short term.

Hope this helps a bit.