As you've already found out, cross-border one-way rentals are expensive.

Do you actually NEED a car? I appreciate that travelling with a small child makes train travel slightly less convenient, but unless you're planning on touring rural areas you really don't need a car in Germany or the Netherlands. You definitely don't want a car in places like Munich or Amsterdam - it's a hindrance more than a help.

As regards cost... if you're going in a couple of weeks you've probably left it a bit late, but saver train ticket to Amsterdam can be had from as little as 19 Euro each from the towns you mention. Saver tickets go on sale three months before the date of travel, and just like with air travel the lower fare buckets tend to get snatched up very quickly, so you're probably out of luck now... but you can always try (www.bahn.de)