I usually use Google XML Sitemaps, maybe the most used plugins to generate XML sitemaps on WordPress. Unfortunately, this nice plugin doesn’t work on WP Multisite. And it doesn’t generate multiple sitemaps.
If you want a XML sitemap plugin to generate sitemaps on your multisite wordpress, you want try WordPress SEO by Yoast, as far as i know the only plugin that works well in generating a sitemap on a WP multisite website.
But if you have a huge website, with thousands and thousands of URLs in it, you may have another kind of issue. In fact, none of the above mentioned plugins generate multiple sitemaps (and the sitemap index, of course) in case you have more than 50.000 URLs to list. And by the way, 50.000 is the limit in the protocol, but Google seems not to love sitemaps with more than 10.000 URLs listed. If you have this issue, you should try Strictly Google Sitemap, a plugin that allows to generate multiple sitemaps (and with great performances!). Only problem i found out using this plugin is that the permalink structure must include some numeric value (%post_id%, for example), or the sitemap generated won’t be correct.
And if you have a WP multisite with some of the websites in the network with more than 50.000 (or just 10.000) URLs? I’m afraid we have to wait for it: i couldn’t find any.