My brother has filed I-130 for me and it has been approved with USCIS and it is now with NVC but my I-94 expired for 5 months. The question is what should I do next shall I wait until I get the visa number and apply form I-485 for adjust of status.

You should leave US immediately. If you overstay longer than 6 months but less than 12 months, you will be barred for 3 years.

Since your petitioner is your brother, you will have to wait for visa number approx 10 years.

If I leave US how long will it takes to get the visa number my priority date is June 15th, 2003. If I overstayed do I have anyway to apply to avoid the penality

The current priority date for FB-4 for most countries is October 15, 2001 so you have some time to go. As you are currently an overstay, you are ineligible to adjust status in the US unless you are grandfathered for section 245(I) or are eligible under 245(a).

I agree with Lawanwadee, leave ASAP to avoid the 3/10 year bar. Even now, you will need a waiver as you have an immigration violation with your overstay. With a 5 month overstay plus the time allowed under your I-94, many officers will assume you also worked without authorization.

What visa did you use to enter? this could be very important. Consult with an experienced immigration attorney immediately.