Unfortunately there are not that many Malaysian or Indonesian restaurants in the city. In my 20 years or so living in NYC, there are only a few that I'd consider decent to pretty good. Here's my list:

Malaysian:

NYONYA
194 Grand St
Btwn Mulberry and Mott Sts, Chinatown
212 334-3669
One of the best in the City with authentic dishes , not creative fusion. Great Roti Canai, Laksa and Nasi Lemak.

NEW MALAYSIA
46-48 Bowery
Chinatown Arcade btwn Bowery & Elizabeth
212-964-0284
Very, very good dishes. The Prawn Mee and Chicken Rice are quite nice.

Indonesian:

MINANG ASLI
86-10 Whitney Ave
Flushing, NY 11373
718 429-8207
Take the R train to Elmhurst, Queens
This hole in the wall restaurant, 20 minutes away from Manhattan, is really worth the trip. They have the most delicious RENDANG outside of Indonesia (Heck, it even rivals some of the best in Indo). They even serve Durian Juice!!! (yum!) Truly recommended!
http://events.nytimes.com/2006/02/01...ws/01unde.html

BALI NUSA INDAH
651 9th Ave
Btwn 45th & 46th St
212 974-187
The only Indonesian restaurant in Manhattan that is not mixed with other SE Asia cuisine. Food is decent, if not bland at times. They do serve rijstaffel, but it's nowhere as good or as extensive as those found in Amsterdam (which is by the way, in a true spririt of FT, only a 7 hour flight from JFK ) Good for a quick fix if you're in Manhattan and don't feel like going to Queens.