Q:

What Hindu Scriptures say that Universe has diameter of fifty crore yojana? 

Srila Prabhupada said that humans never went to Chandraloka as it requires enlightened soul and opined humans might have gone to other planet such as Rahu.  He said whole universe is panchshat-koti-yojana which means fifty crore yojana or panchashat or four billion miles in diameter.  
Can i know which scriptures (preferably vedas or upanishads or puranas; not the work of Astronomers such as Aryabhatta) cite this calculation? 

A:

I think Prabhupada is stating diameter of Universe from this verse of Srimad Bhagvatam:

एतावाळ् लोक-विन्यासो मान-लक्षण-संस्थाभिर् विचिन्तितः कविभिः स तु । 
पञ्चाशत्-कोटि-गणितस्य भू-गोलस्य तुरीय-भागो ’यं लोकालोकाचलः ।। ( SB 5.20.38) 
  Learned scholars have thus described the planetary systems and their particular symptoms, measurements and locations.  By mathematical calculation it comes that Lokaloka is situated at one fourth (Turiya Bhaga) of this Physical Universe (Bhumandala) which has diameter of 50 crore yojana (PanchaShat Koti). 

That verse states: 

पञ्चाशत्-कोटि-गणितस्य भू-गोलस्य। 
  Bhu Gola (Mandala) is mathematically calculated as 50 crore (Yojanas). 

As a side note it is not necessary that 50 crore Yojanas is equal to 4 billion miles.  Value of Yojana is a debated value.  Also it may be cosmic Yojana.  Also it maybe diameter of BhuMandala during Saraswata Kalpa as Bhagvatam narrates the Story of Saraswata Kalpa.  Also the term Koti usually means millions but it isn't necessary that it always means millions.