Can I work and stay in the US permanently with the visa called EB-3?

The EB-3 is an immigrant visa classification (green card). yes you may remain and eventually become a US citizen if that is your choice.

What can be done if a person is married to a US citizen, but didn't come in legally?

It is very likely a trip outside the US will be required to obtain resident status. The unlawful entry prohibits filing for adjustment in the US...

Can we change our visa to B-1 B-2 status (business/ tourist visa) or have a working visa?

You may file for a change to B-2 visa but it will be difficult to obtain an approval. For most employment status you need an employer to petition...

Can I get an E2 visa?

An E-2 requires among items that you are from a treaty country and that you are making a substantial investment in a business.

if my sister were to live in the USA with a tourist visa for about 3 months, will I be able to petition her as a resident?

As a US citizen you may file a petition whether in the US out outside the US. Your sister will have a many year wait and will need to wait outside...

Can I apply for the green card while I'm on a pending status? What should I file?

If your spouse is a US citizen and there are no other bars, yes.

As my clolleagues note, send a copy hold the original for the interview or when asked.

Will the I290B affect my tps renewal or is that two different cases and has nothing to do with each other?

The two I290 and TPS do not affect each other.

The petition should be an immediate relative I-130 as your stepson, not a K-4.

1) If H1B Amendment is still in process upto the month may then what should I do ????? because my I94 expires on May.

You may remain employed until 240 days elapses or approval. If denied your employment ends. Best to speak with your employer's immigration attorney...