1) if i power up the board with 5V , will the JTAG pins logic levels are nearly 5V? or it can be 3.3v?
JTAG Adapter uses the VTARG to detect the operating voltage of the target and then drive the JTAG pins with VREF. So, if the board is at 5V, JTAG pins will be driven at 5V.
2) can i use "J-LINK EDU MINI" as programmer for this chip as i already own it, but the datasheet of j-link edu mini states that to use it with 3.3v and as i already stated that my CY8C5467LTI-LP003 will be powered up with 5V.
The J-Link EDU Mini supports target voltage upto 3.3V only, you can have a look at it here. PSoC54LP has operating range of 1.71 to 5.5V. The voltage levels of Host Programmer and the PSoC 5 voltage domains involved in Programming should be same. So, please set the operating voltage of your board to 3.3V and then you should be able to program. I don't have the J-Link EDU Mini adapter, so I cannot confirm.
3) is there any JTAG programmer for this CY8C5467LTI-LP003 chip from cypress? will it work with my chip if i powered up my chip with 5V?
Cypress provides the Miniprog3 programmer/debugger which can be used to program using JTAG. Yes, it can work at 5V.
4) "CY8CKIT-059" this have "KitProg" biult on the board which can be separated from the main board , my question is that , is that possible to use this KitProg to debug/program any "CY8C5467LTI-LP003" chip? is that KitProg having JTAG pins? or just SWD?
Yes Kitprog can be used to program your board. But note that Kitprog is an onboard programmer/debugger which has been tested and guaranteed to work with Cypress Kits. For custom boards, we recommend using Miniprog3. Also note that Kitprog only supports SWD.