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Kind of a good-news/bad-news situation: Chicago has a big public housing system to help support homeless and low-income people, particularly families, but there's a huge amount of demand for it and waiting lists are often on the order of decades. You may have a higher priority if you're a senior citizen or are currently experiencing homelessness, but the wait times are still Not Great.
However, there are also a lot of nonprofits that operate their own low-income and supportive housing in the city. Combing through them for ones that match your needs can be time-consuming but can pay incredible dividends; just be prepared to contend with information only distributed by phone, outdated phone numbers, no-pet policies, referrals required, and (shorter) wait lists on your way, and don't give up after the first few.
The Chicago Housing Authority (CHA) operates public housing and voucher programs on behalf of the City of Chicago. You can view wait times by property on their website; ones with more specific requirements have significantly lower wait times (e.g., one set aside for homeless new moms has a 0-3 month wait time, compared with some properties having a 25-year wait); studio apartments also have a much shorter wait time on average (many are at about 1-3 years, which is a solid backup plan if other options don't pan out).
You should submit an application to the CHA. But you should also line up other options, since those may be accepting applications immediately or have much shorter wait times.
Mercy Housing - operates a number of properties in Chicago. Despite the name, does not have any religious requirements for living there. Buildings have their own individual policies (some do allow pets) and rental amounts; some are specifically oriented toward certain populations (e.g. families; PLHIV; formerly homeless; in substance recovery; seniors). You will have to call properties individually on the phone to find out how to apply.
Affordable Housing Online Chicago List - Larger website that keeps track of affordable housing properties nationwide. If you scroll down on an individual property page, has lists of income requirements, notes on amenities, and info about who manages the property.
Chicago House - among other services, provides housing to people living with HIV and their families.
Sarah's Circle - has units available for permanent/long-term housing. Women only; note that I do not know how friendly it is to trans women and transfems.
Center on Halsted Homesharing - matches LGBTQ young adults and seniors to share living space for intergenerational companionship.
Chinese American Service League - Provides help with applications to subsidized housing, referrals to legal aid, tenant's rights assistance, property tax appeals, foreclosure prevention, and renters' workshops. Seniors can receive small free home repairs.
The Night Ministry - specifically oriented toward homeless teens and early twentysomethings (and any children they might have); also has a subsidy program to help the transition to permanent housing.
Chicago Connected - If you have a Chicago Public Schools or City Colleges student in your household, you're eligible for an internet service discount. There used to be a low-income federal program for internet access across the board, but it's out of funding and no one knows if it will ever be funded again. Also has information on programs for getting free home computers based on income requirements.
Electricity and Heating (LIHEAP) Assistance - The Low Income Home Energy Assistance Program (LIHEAP) is a federal program, but the Greater Chicago Food Depository can help with LIHEAP applications (as well as EBT and Medicaid). You can ask them to give you a call with this form.