We brought our daughter to The Polliwogs at Suntec. They have a separate area for younger kids and there's a bouncy castle too. The other section is for older kids and there's a mini cafe-like area for adults. It can get pretty crowded so might want to be careful and watch out for yr child as the older kids will run amok. Fidgets City @MBS seems popular too.
You can check out cheekiesmonkies.net for family activities (indoor and outdoor). My friend, the author of the blog Kevin Ang has published a guide book titled 'Got Kids Go Where' for his blog compilation. You can get the book from Mothercare Store and get wonderful suggestion from him.
Cool-de-sac at Suntec is another good one. There are separate zones for all activities so much safer to have little ones there. Our kids love the ball pool and the toddler area at Amazonia. It also has one of the nicer cafes for parents.... :)
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http://www.amazoniafun.com/ Amazonia was great fun for pre-schoolers! Try to go on weekdays as it will be less crowded.
I personally like Kids Amaze at Toa Payoh. They have a nice play area for toddlers and a huge play area for older kids.
There's a new indoor playground at Centrepoint called http://littleplanet.com.sg/. You can check it out.
thanks